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Density plots post hard-filtering, good enough for VQSR resource?
I am trying to hard filter a variant call set using, as a first approach, the following thresholds, according to a related publication I found:
QD < 2.0 | FS > 60.0 | MQ < 40.0 | MQRankSum < -12.5 | ReadPosRankSum < -8.0
As I understand it, after going through the GATK documentation on hard filtering, there are no set rules to tell that the variant call set was (hard) filtered properly, other than visual inspection of the density plots, which requires experience.
For this reason, I would like to kindly require your inputs on the following plots, in order for me to see what are the next step I should undertake.
This is what I would venture:
QD: leave it as it is, enough variants filtered.
FS: according to log10 scale, leave it as it is, enough variants filtered.
MQ: may need higher stringency.
MQRankSum: according to log10 scale, leave it as it is, enough variants filtered.
ReadPosRankSum: according to log10 scale, leave it as it is, enough variants filtered.
Add SOR > 3.0?
I must mention that I want to use this variant call set as a resource for VQSR.
Thanks in advance!